


Blue Blood, Red Blood

by TimeSpaceBlueSkye (orphan_account)



Category: Agents of S.H.I.E.L.D. (TV), Doctor Who (2005)
Genre: Clara is in love with Twelve, Coulson has a huge crush on Skye, Crossover, Doctor and Coulson get along really well, Enjoy the story, F/M, Gen, Nobody likes Grant Ward, Nobody wants to admit it, Other, Post San Juan, Skye and her dad get to know each other, Skye's huge crush on Coulson, Twelve is in love with Clara, Unresolved Romantic Tension, skye's powers
Language: English
Status: In-Progress
Published: 2015-02-16
Updated: 2015-03-04
Packaged: 2018-03-13 07:43:07
Rating: Not Rated
Warnings: Creator Chose Not To Use Archive Warnings, Graphic Depictions Of Violence
Chapters: 4
Words: 4,579
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/3373373
Author URL: https://archiveofourown.org/users/orphan_account/pseuds/TimeSpaceBlueSkye
Summary: <blockquote class="userstuff">
              <p>The Doctor and Clara find a strange object in Sao Paulo. Skye shows up to confiscate it and take them in.</p>
            </blockquote>





	1. Don't Touch

**Author's Note:**

> So, this is the first fanfic i've done for this site. To be honest, I'm a little scared. I know i'm not the best of writers but i couldn't get this out of my head.

**Notes for the Chapter:**

> Soo this is my first fanfic on this site. It's a work in progress getting used to the setup here. That being said I like it much better than the site I used before. All of the graphic scenes will be coming later in the chapters. It's pretty clean for now.

"What is it?" Clara's eyes peered over the Doctor's shoulder at the long metallic object in his hands. 

"I dont know." he stated flatly and a look of surprise crossed Clara's features. Rarely did the Doctor ever _not know_  something. She couldn't help but grin at the frown that deepened his features.

"So, what is it doing on earth?" she queried. 

"What does that mean?" the Doctor looked at Clara and eyed her with something between amusement and annoyance. "Why are you assuming its alien? Why can't this be some new form of artwork that another one of you pudding brains made up?" He smirks at that, but freezes when he catches the glare that he is receiving from Clara. 

"Doctor, we are humans not pudding brains." She bites out trying to make her words sound like ice. _God, he was insufferable_. "Besides, just look at those symbols. We can't make things like that just appear. Not yet, at least." She glances up at him to see his brow furrowing in thought. Clara sighs, trying to hold back the urge to reach out and run her fingers along the hardened lines of his face. Really, he could be so _distracting_. 

"Right." he said, bringing her thoughts back to the strange object he held in his gloved hands. 

"Can I see it?" she asked, a tentative smile creeping onto her face. He held it out to her and she reached out to wrap her fingers around the metal but she never finished the action.

"Don't!" someone yelled from behind her and both her and the doctor jumped. "Don't touch it!" _American_. Clara recognized the accent and turned to face a young woman. She was standing at the door with a small pistol trained on the Doctor. "Put the obelisk down." She bit out, and the Doctor followed her order, setting the metallic object on the table. He gave Clara a puzzled look before turning back to the woman at the door. "Hands up. Where I can see them...Good. My name is special agent Skye, with S.H.I.E.L.D. You two are coming with me."

* * *

When Skye received the call on her weekend off she really wasn't surprised. She knew that three days away from crazy gifted psychopaths and nazi mercenaries was almost too good to be true. That being said, her mood wasn't the greatest when she arrived at Sao Paulo to investigate some Hydra activity there. What she found, clearly, was something that she did not expect. Icer in hand, She stood just outside the entrance to a small shack just outside the city. She listened with amusement to the conversation going on inside.  _Did he just call humans pudding brains? If these people are Hydra, why don't they know what the obelisk is? What does that mean, not yet?_ She tried to make sense of the bits and pieces that she picked up but then she heard the woman ask to see it. Oh.  _Oh._   _No one else can die like Trip. Even if she is Hydra._ That is when she stepped through the entrance, saying the first words that came to mind.

"Don't! Don't touch it!"

 

 


	2. Remember When?

**Summary for the Chapter:**

> Skye returns to the Playground with 12 and Clara, and then has a chat with Coulson.

**Notes for the Chapter:**

> This chapter is alot longer than the previous one...Hope you enjoy it.

The Doctor was not thrilled. Ok, maybe a little intrigued to say the least, but, he by the time the mysterious young woman had taken them both into custody, he was thoroughly confused. She kept asking him questions about a Greek mythological creature with lots of heads, aliens and special powers, and something about the rain,  _No, She said Raina. Which means she's a person?_ His patience was wearing a bit thin, and all of these new questions were not helping to appease him. Most of all, he was worried about Clara. She was silent the entire time and her face had done the all-eyes thing again.  _At least she isn't so pale now._ And he couldn't help but think that clara looked beautiful even when she was pale... _No. Stop it. She'd said it herself. That could never work out._ He sighed and decided to distract his thoughts by getting some of his questions answered. 

"Where are you taking us?" 

"That's classified." He almost thought he could see a smirk on her face when she said that.

"Good. Classified. I've always wanted to go somewhere called  _Classified._ " This time he didn't hide his smirk when she turned to look at him. Shaking her head at him she replied,

"You honestly have no idea what this is about, do you?" The doctor frowned in reply.

"You were in possession of an O-8-4. And you had no idea what it was or how it affects people, affects  _humans,_ and you were gonna let her touch it? I'm glad I stepped in then." Skye saw his eyes widen at that thought. So, she'd guessed right. Eyebrows did have a soft spot for the woman. She needed information. She couldn't just bring these two people back to the Playground without being  _absolutely_ sure that they weren't working for Hydra, or Ward, or Raina, or whoever else had it in for S.H.I.E.L.D. these days. Honestly, she couldn't keep track. 

"It would have killed her. Turned her into stone. Kind of like Medusa." He scowled at that and turned to the woman.

"Clara, I would never...I didn't mean...I'm so sorry."

"Doctor, It's alright. I know you'd never hurt me willingly." The Doctor,  _So that was his name,_  seemed to visibly relax at that point. 

"Doctor? Doctor who?" Something between a chuckle and snort came out of Clara's mouth.

"That's what I've been asking since day one, literally." Skye smiled at that. She couldn't help but think of all the times she had spent wondering what her real name was.  _Daisy._ It almost felt weird to know now, that being said she hadn't told anyone about it.  _I'm Skye. Always have been, always will be._ That being said, the only person who knew was Coulson, because he'd been there when her father had so gloriously announced it to her before running from the room. And then she'd gone down into that  _stupid city_ and gotten herself  _and Trip, don't forget that he wouldn't have been in there if you hadn't gone after Raina,_ and had her entire being changed into something that had taken her months to contain, to control. She shuddered at those memories now. _  
_

"Are you okay? You've gone pale." Clara asked. Her voice crashed through Skye's reverie and rooted her back in the present. 

"Yeah, I'm fine." 

"What about you then?"

"What about me?" 

"You know our names. What is yours?"

"I told you. I'm Skye."

"Well, yes but, Skye what?"

"Skye, just Skye." 

"I bet there's a story behind that." Clara had this look in her eyes that Skye couldn't quite classify. It said something like,  _I'll get it out of you yet._ And that thought alone made her decide on her next actions.

 

"I'm going to take you in for questioning." She stated flatly. 

"You mentioned that already." Skye looked at Clara as she fingered the Icer in her hands. 

"I'm sorry, but you can't know where that is." she said before raising the gun and firing twice. They both dropped to the ground at nearly the same moment. But it was how they fell that brought an amused smile to Skye's face. She wasn't being creepy or anything, smiling at them falling asleep, but right before the Doctor fell, he'd grabbed Clara's hand and from the looks of their already whitening knuckles, Skye was going to have a difficult time separating them.

"Eagle this is Skye. I have the package. Ready for extraction." she said raising a finger to her ear.

"Skye, you know it's me. Why do you have to refer to code names?" May's voice rang clear through her ear piece.

"Because it's just way cooler that way." She could almost her May's frown over the comms.

* * *

"Hey, AC, what's up?" Coulson smiled. 

"You know technically that doesn't apply to me anymore." He replied with a smug grin on his face. 

"Yeah, I know. But DC doesn't suit you." He laughed. 

"So, you picked up some guests?"

"Oh. right. Yeah. Is that okay? I don't think they are particularly dangerous, and I know they had the obelisk, but they didn't have a clue as to what it was. And they were really confused when I started talking about Hydra and all that."

"I trust you, Skye." Skye couldn't help but feel a flush of heat come to her face. 

"Of course you do." She replied with a slight smile on her face. "Oh, which reminds me. I got something for you." Coulson looked up at her from his desk. She was excited, he could tell, as she sat at the end of her chair with a beautiful smirk on her face.  _beautiful? where did that come from?_ but Coulson knew. He knew he'd been thinking about Skye way to much lately. Well, not exactly lately. He's been thinking about her in a way that was less that appropriate ever since he'd held her in his arms in Quinn's basement and the thought of losing her, losing  _Skye_ , had terrified him, to say the least. 

"Happy Anniversary." She said, and held out a small object in her hands. 

"Happy what? ...Oh my god, Skye. How did you?" His voice trailed off as he picked up the watch from her hands. It looked just like the one he used to have. Before he had to use it to blow a hole in the door and escape. He remembered telling Skye to drop it and run if anything started to leak out of it. _This doesn't sound like a watch!_  She'd said. and he couldn't help but smile.

"It's been two years since you invited me to stay on the Bus. I figured it called for a celebration, so Happy Anniversary." She grinned when his eyes lit up as he caressed the contours of the watch.

"It's just like it. How did you find this?"

"What did you think I did on my time off? I'm just glad I found it before you called."

"Thank you." he said and the smile on his face was so genuine that Skye's heart skipped a beat. _No, Skye. He doesn't think about you like that. He's traditional, and he likes god damn protocols. He thinks of you like his daughter, not like that._ Desperate to get her mind of her thoughts she changed the subject.

"So, I guess we have guests then?" 

 


	3. Who are you, really?

**Summary for the Chapter:**

> The doctor and Clara are taken to the Playground. Interrogations ensue.

**Notes for the Chapter:**

> Since I completely forgot to do this in the beginning, I don't own any of the characters. I wish I did but...yeah.

When the Doctor opened his eyes, he briefly registered a flash of blue before his vision cleared. He was in a room covered in metallic octagonal panes. Skye was sitting across from him with an expectant look on her face.

"Sorry about that. We can't afford to have our location known." She told him.  _Was she smiling? This isn't funny. Not funny at all. Once Clara wakes up he's going to...Clara!_

_"Where's Clara? If you have done anything to her-"_

"She's fine. Just being interrogated separately."

"I want to see her."

"You will. Just answer some questions for me first."

"I don't take orders. You will take me to Clara. You will let us go from this compound, and then I will think about not making the rest of your lives  _very_ miserable." The doctor leveled an icy glaze at Skye, who returned the expression in like fashion.

"Listen,  _Doctor_ , do you even know what you were about to let your precious Clara do? Are you even aware of what an obelisk can do to a human? I saved her life! If I wanted to harm either of you, to harm her, I would have let  _you_ do my dirty work for me." 

"I don't believe you." The Doctor said, keeping his voice at a calm rage. Skye, on the other hand, was not so subtle.

"I told you already that she would have been turned to stone. She would be dead right now if I hadn't stepped in. So shut up, and listen to me." Skye sucked in a deep breath. Yes, she had control over her powers, but they were still closely tied to her emotions. They had been born in the flood of emotions that Skye was experiencing when the obelisk opened, and anger always made her react in some way. She could feel the tremors in her body and hoped to god that she wasn't letting them out. The Doctor showed no indications that he could feel anything resembling an earth quake but he did look  _extremely_ pissed off.  _Good. Pissed off I can deal with. Narcissistic, know-it-all Scot? THAT was crossing a line._  

"I am going to ask you some questions, and you are going to answer them to the best of your ability. First question, Doc, what were you doing with that obelisk?"

"My name is  _Doctor_ not Doc, first of all, and I was unaware that I had to explain everything that did to you pudding brains every time I passed by. I certainly did not know that I would be interrogated for investigating a possible alien threat. Maybe next time I'll let the Sontarans take your planet over."

"So, you were just checking it out? Not using it as a weapon?"

"Yes. I believe i have made that much very clear."

"Are you an alien?" Skye asked, a hint of a smile played at her lips.

"Are you?" He asked, almost not bothering to hear her answer.

"Yep. Part Cree on my mom's side actually." The doctor's head whipped up.

"You're an alien?" He asked, his voice raising to a higher pitch as his curiosity grew.

"Don't look so surprised Doc. Now I asked you first."

"Yes. I am. I'm a timelord." Skye grinned.  _Timelord? Now that's not pompous at all._

"Was anyone else besides you and Clara in that shack before I arrived?" 

"Well, Clara and I found it because we had been following a group of Zerians. They met up with a lady in the shack, talked alot about power, and world domination, and people dying, and then left. Clara and I went in after that. You know the rest." 

"What did the woman look like?"

"She was short. Wore a veil. Had lots of curls. Her fingers were more like claws than hands, but that is just my opinion. She wore a dress covered in flowers." 

"Raina." Skye breathed. "Thankyou for your help Doc. I'll take you to Clara now if you want." The Doctor merely nodded his head and stood up.  _Funny, I didn't even realise i had started cooperating._ Oh. He had been played, and played well he might add. This Skye, strange and intriguing as she may seem, definitely knew how to get the information she desired.  _  
_

 

 

When Coulson reached the interrogation room he was surprised, to say the least, by what he found. He'd been expecting hard core mercenaries or former agents, not someone who could very well pass as a school teacher. 

"Hello. I'm Agent Coulson. I just want to ask you a few questions and then you can go see your friend." 

"Clara." the woman said as she took the hand that Coulson had offered her and shook it firmly.

"I'm sorry about the methods we had to use to get you here. It is important to us that our location remain a secret." Clara rubbed the spot on her arm where she had been tranquilized. 

"Next time, you should ask before shooting and kidnapping me and my friend."

"You were shot with a dendrotoxin. It induces a sort of dream state. You fell asleep, nothing more."

"I know." She said. And boy did Clara  _know._ For once she was glad that the Doctor wasn't here, because after the dream that she'd been having? She wasn't sure she could look him in the eye without giving everything away.

"Can you tell me what you and your friend were doing in Sao Paulo?" Coulson asked, and pretended not to notice the blush that had flushed her cheeks.

"Well, we were  _supposed_ to be enjoying a nice, relaxing vacation at a local resort. But nothing is ever relaxing with the Doctor, so when his sonic picked up traces of alien DNA, we tracked down the Zerians to that shack. Then, your agent came in and, well, here we are." 

"You have the technology to track alien DNA?" 

"He can. He blames it on the sonic but I've seen him without it and he just...knows. He isn't human. He's a timelord. I'm not sure if that means he can sense these things or not but whatever it is, it works."

"Thank you for your time, Clara. I appreciate your cooperation." 

 

 

Skye was amused to say the least as she watched their reunion next to Coulson. Clara had ran to the Doctor and encircled his neck in a hug that would have put bears to shame. The poor old man seemed so confused and unsure of what exactly to do for a moment until he gingerly rested his hands on her back and rubbed small circle's there. When the embrace was finally broken, Skye noticed that Clara's hand was grasped firmly in the Doctor's, much the same way as it had been when she'd iced them. That made Skye smile.  _They really care for each other don't they._ She was still thinking about that tender touch when Coulson broke through her thoughts.

"Skye...Skye?" He waved his hands in front of her face and she started, looking at him with wide eyes. "Woah. You really spaced out there. You okay?"

"Yeah, I'm fine AC. Just lost in thought I guess." Skye heard Clara chuckle behind her. 

"AC?" She asked and Coulson smiled. 

"Skye isn't really in to full names." 

"No kidding." the Doctor said and gave Skye a look full of disdain.

"Oh come on, Doc. It's not that bad. You'll get used to it." Skye was pretty sure Clara had chortled at that.

"Used to it?" the Doctor replied. "I thought we were free to go?"

"Well, you are. Free to go, that is. But if you want, we could use someone with your...talents to help us figure out what Raina is doing with an obelisk. You can stay on the Bus, or here in the Playground if you like. S.H.I.E.L.D. can always use allies, and I get the feeling that you want to know more about that obelisk. What do you say, Doctor?" Coulson asked. The Doctor looked thoughtful for a moment. 

"Alright. We'll stay. But I'm going to need my T.A.R.D.I.S. It's a big blue box at these coordinates." He stated flatly, but Skye could see a faint hint of a smile on his lips. 

"Come with me," Coulson said, "I'll take you to Simmons. She did all of the primary research on the obelisk when we were studying it. If you have questions, best to start with her." and with that, the Doctor and Coulson left the room. Skye turned to Clara with a sheepish look on her face. 

"I'm sorry I had to shoot you. I couldn't take the risk-"

"I understand." Clara smiled, "I don't think we've properly met. I'm Clara Oswald, and you're Skye. Now, tell me that long story you mentioned earlier." When Skye responded with a thoroughly confused look Clara sat down on a couch and motioned at the space next to her. "You said your name was 'just Skye' I bet there's an interesting story behind that." She said with a warm smile that made Skye feel like she could tell Clara anything; so she did. As Skye narrated her story the thought entered her mind that only Coulson made her feel like she could tell him anything, and Skye didn't even do that as often as she would have liked. So what made Clara Oswald so different? What made Skye trust her so completely?

 

 

**Notes for the Chapter:**

> Thanks for all the hits, comments, and kudos so far. It means alot. If you have any feedback or questions that I can clarify (without spoiling the rest of the story) Please ask in the comments. 
> 
> Smiles all around, people.


	4. Dad, I'm Home.

**Summary for the Chapter:**

> Skye goes to her father for answers about Raina.

**Notes for the Chapter:**

> Sorry it took so long to update. I've been busy with school and whatnot. Hope you enjoy this bit. Contains spoilers for tonight's episode.

"And this is where May and I train, every morning at five. And over there is the garage and the lab. It's not much but this has been home for the better part of two years for me." Skye was just finishing giving Clara a thorough tour of the Bus and Playground.  _So many memories._ After her very unexpected and extremely thorough heart to heart with Clara she decided to lighten the mood with just a bit of domesticity. Coulson and the Doctor were still talking with Simmons about the obelisk so Skye had taken Clara to meet the team.  _  
_

"You've got a wonderful family." Clara said to her.

"I know. It's taken alot from all of us to get here. But we've all gained so much. In the end, we'll have each other, and that will always count for something." 

"You'll always have each other? Now that's not sappy at all." Skye noted the teasing grin on Clara's face with a sarcastic gasp in return.

"And what's wrong with sappy? I seem to remember a few  _very_ sappy moments between you and Doc. Don't lecture me on sappy Oz."

"It's not...he doesn't...we, we aren't like that. We're not  _together,_ we're just friends." 

"Stuck in the friend zone then? Is that anything like being stuck in the adopted daughter zone? If so, then I know how you feel." Clara chuckled.

"You and Agent Coulson aren't..."

"Together? No. But I'm not against the idea of me and AC being...more. But I think he thinks of me like his daughter. Which sucks honestly, because I have a dad. Granted he is slightly unstable and a little obsessed but I've made it this far without real parents in my life. I wish he could see that."

"See what?" A deep voice said behing her.

"Jesus, Mac, don't do that to me." Skye threw a light punch into his shoulder.

"Clara, this is Mac. Mac, this is a guest. Be nice." Skye shot Mac a pointed look.

"Good to meet you Miss Oswald. I'll have you know that I am always a courteous person, despite what Agent Skye tells you." that earned him another punch. 

"Always a pleasure, Mac." Clara grinned and Skye let out an exasperated sigh when May walked in.

"What's wrong, Skye?" May asked. 

" _Him."_ she said jerking her thumb in Mac's direction. He chuckled.

"Skye says that I'm not nice." A grin spread wide across his face. 

"Skye?" May asked and Skye saw the question there without it being spoken.

"Oh for God's sake, get a room you two!" She grabbed Clara's hand and left the room before they  _actually_ started making out. 

"So, those two are um?"

"Inspector Gadget and Mulan? Yeah. Talk about sappy." 

 

* * *

 

 

"We need to find out what Raina is up to." Coulson was saying. "What does she need the obelisk for so badly?" 

"They did talk about using it to change something...or someone. I wasn't really listening to their conversation." The Doctor tried to appear nonchalant at that statement but felt that Coulson could see right through those words to the reason he hadn't been listening. The reason being Clara's ear pressed to the door, her breath coming in short waves as she tried to understand what was going on inside. At least the rest of the people there seemed to take the bait. 

"Is there anyone you know who was close to Raina? Someone who could understand what she is up to?"Clara asked.

"Well I could talk to my-"

" _Skye._ "

"What, AC? He would know what she wants. He knows what she is doing."

"I know but your father is..."

"Delusional and mentally unstable? Coulson, he'd never hurt me. Which is why I'm the one who should go. I can get the answers we need without making him go all Dr. Jekyl and Mr. Hyde on me." Skye said. 

"I'm with Skye. He won't listen to anyone else." May said. 

"Fine," Coulson sighed. "Suit up, Skye. We owe your father a visit."

* * *

 

 

It hadn't taken that long for Skye to locate her father. He'd made a point of not hiding from S.H.I.E.L.D. anymore. So, Skye was sitting in a diner in Memphis, waiting for the man who was hell bent on killing the man who she cared about. She decided not to focus on how messed up that sounded in her head when a familiar Scottish accent broke her thoughts. 

"Don't worry. Everything will be fine." 

"Doctor? What the hell are you-Actually, where the hell are you?"

"I'm right next to you, just invisible. "

"You're invisible? Ok. That is so cool. How are you invisible exactly?"

"It's a watch. Makes whatever is behind me, appear in front of me. He wanted to come but I reconfigured it to only work with timelord DNA after..." His voice trailed off and Skye couldn't help but notice a hint of jealousy lying behind its low timbre. 

"Are comms up yet, May?" She said. 

"Yes they are."

"Coulson? Where's May? I thought she was going to be on the other end for this op."

"Yes, well given the nature of the op I decided we should all be a part of this so the whole team is here. I didn't want you to face this alone."

"Well, I'm not alone. There is a certain invisible timelord who joined the party." She heard a groan over her comms.

"I told him to stay quiet. I told him to not engage you under  _any circumstance."_

"Yeah, about that, he doesn't listen very well to orders." she heard Clara say. She was chuckling slightly when a familiar figure walked through the front entrace. 

"Alright, it's game time. He's here." She said over her comms as she waved at him from her booth. He walked uncertainly towards her with a tentative smile on his face. 

"I thought that you never wanted to see me again, after I..."

"After you used me as bait to try and kill Coulson? Yeah, me too."

"So, what changed?" He asked.

"Raina." she said and studied his face carefully. His face showed a mixture of anger, confusion, and disgust.

"You need information." he breathed and Skye nodded. 

"What would she want with another obelisk?"

"We parted ways after San Juan. I haven't seen her since."

"That's not what I asked." Skye stated flatly. 

"Skye, I'm sorry. I didn't mean to cause you so much pain. I didn't think that she would be such a problem. I just wanted you. I was so angry with them for taking you from me. I'm so sorry." And Skye really wouldn't have been alarmed, except for the fact that he said those words like it was for something that he hadn't done yet, like he was about to do something that he was already regretting.

"I have to show you the way." He said before he pulled out a small object and pressed a button. Skye couldn't really comprehend what happened next. She just knew that it  _hurt._ Whatever that object was, it was doing something that made her blood boil, her ears ring, her entire nervous system was going haywire. She couldn't feel, couldn't move. Suddenly, she was surrounded in a blue light. The last thing she saw was the face of a man without eyes before her vision went black.

**Notes for the Chapter:**

> Cal's device comes from a bit of inspiration from The 100.


End file.
